The Rice Restorer Rf4 for Wild-Abortive Cytoplasmic Male Sterility Encodes a Mitochondrial-Localized PPR Protein that Functions in Reduction of WA352 Transcripts

Tang, Huiwu; Luo, Dangping; Zhou, Degui; Zhang, Qunyu; Tian, Dong; Zheng, Xingmei; Chen, Letian; Liu, Yao-Guang

doi:10.1093/mp/ssu047

Cited by 140 publications

(99 citation statements)

References 7 publications

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“…2B). Notably, the RF6 protein contained a duplication of motifs 3-5, which are absent in rf6 or other known RF proteins (18,(33)(34)(35)(36)(37)(38) (Fig. 2B and SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

Pentatricopeptide-repeat family protein RF6 functions with hexokinase 6 to rescue rice cytoplasmic male sterility

Huang

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

130

118

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Cytoplasmic male sterility (CMS) has been extensively used for hybrid seed production in many major crops. Honglian CMS (HL-CMS) is one of the three major types of CMS in rice and has contributed greatly to food security worldwide. The HL-CMS trait is associated with an aberrant chimeric mitochondrial transcript, atp6-orfH79, which causes pollen sterility and can be rescued by two nonallelic restorer-offertility (Rf) genes, Rf5 or Rf6. Here, we report the identification of Rf6, which encodes a novel pentatricopeptide repeat (PPR) family protein with a characteristic duplication of PPR motifs 3-5. RF6 is targeted to mitochondria, where it physically associates with hexokinase 6 (OsHXK6) and promotes the processing of the aberrant CMSassociated transcript atp6-orfH79 at nucleotide 1238, which ensures normal pollen development and restores fertility. The duplicated motif 3 of RF6 is essential for RF6-OsHXK6 interactions, processing of the aberrant transcript, and restoration of fertility. Furthermore, reductions in the level of OsHXK6 result in atp6-orfH79 transcript accumulation and male sterility. Together these results reveal a novel mechanism for CMS restoration by which RF6 functions with OsHXK6 to restore HL-CMS fertility. The present study also provides insight into the function of hexokinase 6 in regulating mitochondrial RNA metabolism and may facilitate further exploitation of heterosis in rice.cytoplasmic male sterility | pentatricopeptide repeat | restorer-of-fertility | RF6 | hexokinase 6 P lant cytoplasmic male sterility (CMS) is a trait characterized by a lack of functional pollen grains in plants, although female gametes are still viable (1). CMS has been widely used to produce hybrid seeds to improve plant yield, improve resistance to diseases or stresses, or enhance taste (2). Plant CMS results from genomic incompatibility between mitochondria and nuclei and is typically associated with an aberrant chimeric gene in the mitochondria (3-6). A specific set of nuclear genes called restorer-of-fertility (Rf) genes, which primarily belong to the pentatricopeptide repeat (PPR) family, repress CMS through the promotion of the cleavage, degradation, or editing of CMS-associated aberrant transcripts or the inhibition of the translation of these genes (7-9). PPR proteins regulate RNA metabolism at multiple levels, from RNA editing, stability, processing, and splicing to translation (10, 11). PPR proteins can be classified into PLS and P families based on the structure of PPR motifs (11). PLS family members generally exhibit direct RNA binding (12)(13)(14) or editing activity (15-17), whereas P-family proteins often lack sites for binding to RNA, particularly mitochondrial CMS-related RNA (18,19). Most of the known PPR proteins implicated in restoration of fertility (RF) are P-family members. Thus, RF-related PPR proteins may require additional partners, such as RNA-binding or splicing factors to process CMSrelated transcripts.Rice CMS is categorized into three major types: Wild Abortive (WA), originating from...

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“…2B). Notably, the RF6 protein contained a duplication of motifs 3-5, which are absent in rf6 or other known RF proteins (18,(33)(34)(35)(36)(37)(38) (Fig. 2B and SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

Pentatricopeptide-repeat family protein RF6 functions with hexokinase 6 to rescue rice cytoplasmic male sterility

Huang

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

130

118

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“…As orf356, orf367 and WA314 have structures similar to WA352a and WA352c, we analyzed whether they also have CMS function. We prepared three binary constructs with MTS-orf356 (MTS, mitochondrial transit sequence), MTS-orf367, and MTS-WA314 ( Figure 2A) and transferred them into a CMS-WA maintainer line ZS97B with normal cytoplasm and the recessive restorer genes rf3 and rf4-i, an indica type rf4 allele [11]. The MTS fusion localizes the protein to mitochondria, thus allowing the test of CMS function using nuclear transformation [10,20].…”

Section: Functional Test Of the Candidate Cms Genesmentioning

confidence: 99%

“…japonica) Nipponbare (Nip) with the recessive rf3 and rf4-j (japonica type rf4), because that the expression of the genes is not affected in the absence of the functional restorer genes [10,11]. Quantitative reverse transcription PCR (qRT-PCR) showed that WA352b, WA352c, WA314, orf367, and orf356 were expressed in various tissues (root, stem, leaf, panicle, and anthers) of the corresponding backcrossing lines (shown in Supplementary information, Figure S3) or Nip (for orf284 and orf314 expression) ( Figure 3).…”

Section: Functional Test Of the Candidate Cms Genesmentioning

confidence: 99%

“…We previously identified the CMS-WA gene WA352 (here renamed WA352c, see below) and revealed that WA352c causes CMS by interaction with the nucleus-encoded, highly conserved mitochondrial protein COX11, leading to premature programmed cell death in the anther tapetum and defective pollen development. Male fertility of WA352c-carrying hybrids can be restored by the dominant restorer genes Rf4 and Rf3, which suppress WA352c function at the mRNA and protein levels, respectively, in diploid anther-wall cells of the hybrids (i.e., in a sporophytic manner) [10,11]. We noted that the WA352c-containing structure in the mitochondrial genome (including the upstream and downstream flanking regions) consists of multiple segments that are homologous to different sequences of the mitochondrial genomes in wild rice species, suggesting a complicated origin through DNA recombination and rearrangement.…”

Section: Introductionmentioning

confidence: 99%

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Multi-step formation, evolution, and functionalization of new cytoplasmic male sterility genes in the plant mitochondrial genomes

Tang

Zheng

et al. 2016

Cell Res

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New gene origination is a major source of genomic innovations that confer phenotypic changes and biological diversity. Generation of new mitochondrial genes in plants may cause cytoplasmic male sterility (CMS), which can promote outcrossing and increase fitness. However, how mitochondrial genes originate and evolve in structure and function remains unclear. The rice Wild Abortive type of CMS is conferred by the mitochondrial gene WA352c (previously named WA352) and has been widely exploited in hybrid rice breeding. Here, we reconstruct the evolutionary trajectory of WA352c by the identification and analyses of 11 mitochondrial genomic recombinant structures related to WA352c in wild and cultivated rice. We deduce that these structures arose through multiple rearrangements among conserved mitochondrial sequences in the mitochondrial genome of the wild rice Oryza rufipogon, coupled with substoichiometric shifting and sequence variation. We identify two expressed but nonfunctional protogenes among these structures, and show that they could evolve into functional CMS genes via sequence variations that could relieve the self-inhibitory potential of the proteins. These sequence changes would endow the proteins the ability to interact with the nucleus-encoded mitochondrial protein COX11, resulting in premature programmed cell death in the anther tapetum and male sterility. Furthermore, we show that the sequences that encode the COX11-interaction domains in these WA352c-related genes have experienced purifying selection during evolution. We propose a model for the formation and evolution of new CMS genes via a "multi-recombination/protogene formation/functionalization" mechanism involving gradual variations in the structure, sequence, copy number, and function.

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“…Several rice Rf genes have been cloned: Rf1 (Rf1a, Rf1b) from Boro II type CMS (BT-CMS) rice (Kazama & Toriyama, 2003;Wang et al, 2006); Rf17 from Chinese wild CMS (CW-CMS) rice (Fujii & Toriyama, 2009); Rf2 from Lead type CMS (LD-CMS) (Itabashi et al, 2011); and Rf5 from HL-CMS rice . Rf3 from wild abortive-CMS (WA-CMS) and Rf6 from HL-CMS have also been mapped and Rf4 from WA-CMS was cloned Tang et al, 2014). A large mitochondrial complex ranging in size from 443 to 669 kDa and containing PPR592, pcf RNA and other factors was first reported in petunia (Gillman et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

The rice DUF1620‐containing and WD40‐like repeat protein is required for the assembly of the restoration of fertility complex

et al. 2016

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SummaryCytoplasmic male sterility (CMS) and restoration of fertility (Rf) are widely distributed in plant species utilized by humans. RF5 and GRP162 are subunits of the restoration of fertility complex (RFC) in Hong-Lian rice. Despite the fact that the RFC is 400-500 kDa in size, the other proteins or factors in the complex still remain unknown. Here, we identified RFC subunit 3, which encodes a DUF1620-containing and WD40-like repeat protein (RFC3) that is present in all tissues but highly expressed in leaves.We established that RFC3 interacts with both RF5 and GRP162 in vitro and in vivo, and is transported into the mitochondria as a membrane protein. Furthermore, CMS RNA (atp6-orfH79) and CMS cytotoxic protein (ORFH79) accumulate when RFC3 is silenced in restorer lines.We presented the analysis with blue-native polyacrylamide gel electrophoresis, indicating that RFC is disrupted in the RNAi line. We concluded that RCF3 is indispensable as a scaffold protein for the assembly of the RFC complex.We unveil a new molecular player of the RFC in the Rf pathway in rice and propose the model of RFC based on these data.

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The Rice Restorer Rf4 for Wild-Abortive Cytoplasmic Male Sterility Encodes a Mitochondrial-Localized PPR Protein that Functions in Reduction of WA352 Transcripts

Abstract: Ahmadikhah, A., and karlov, G.I. (2006). Molecular mapping of the fertility-restoration gene Rf4 for WA-cytoplasmic male sterility in rice. Plant Breeding. 125, 363-367.

Cited by 140 publications

References 7 publications

Pentatricopeptide-repeat family protein RF6 functions with hexokinase 6 to rescue rice cytoplasmic male sterility

Pentatricopeptide-repeat family protein RF6 functions with hexokinase 6 to rescue rice cytoplasmic male sterility

Multi-step formation, evolution, and functionalization of new cytoplasmic male sterility genes in the plant mitochondrial genomes

The rice DUF1620‐containing and WD40‐like repeat protein is required for the assembly of the restoration of fertility complex

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